Deprecated API

Contents

• Interfaces
• Classes
• Methods
• Constructors

Interfaces

Interface	Description
ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao	as Person is deprecated

Classes

Class	Description
ubic.gemma.core.apps.ArrayDesignProbeRenamerCli	renaming probes is not a good idea in general
ubic.gemma.core.apps.MeshTermFetcherCli	should not be part of Gemma main code
ubic.gemma.core.apps.RNASeqBatchInfoCli	this should not be necessary and the regular batch population tool can be used instead.
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser
ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent	this event type was used by the auto-tagger, which has been removed. This event type has been kept so that the audit-trails can still properly display these events, but creation new events of this type should not occur.
ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent.Factory
ubic.gemma.model.common.auditAndSecurity.Person	not needed
ubic.gemma.model.expression.experiment.FactorValueValueObject	aim towards using the FactorValueBasicValueObject. This one is confusing. Once usage of this type has been completely phased out, revise the BioMaterialValueObject and relevant DAOs and Services.
ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl	as Person is deprecated
ubic.gemma.web.controller.common.GemmaClassicHomePageController
ubic.gemma.web.services.rest.util.args.FactorValueValueArg
ubic.gemma.web.util.upload.CommonsMultipartFile

Methods

Method	Description
ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject.trim()	because this is too ad hoc and messy
ubic.gemma.core.ontology.providers.GeneOntologyService.isGeneOntologyLoaded()	not clear this is needed
ubic.gemma.core.search.SearchService.searchExpressionExperiments(String, Long)	use SearchService.search(SearchSettings, Class) with Object.getClass() instead.
ubic.gemma.core.search.SearchSource.searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>)	use SearchSource.searchBioSequence(SearchSettings) (SearchSettings)} instead
ubic.gemma.core.search.SearchSource.searchCompositeSequenceAndGene(SearchSettings)	use SearchSource.searchCompositeSequence(SearchSettings) instead
ubic.gemma.core.util.AbstractSpringAwareCLI.getBean(String, Class<T>)	Use Autowired to specify your dependencies, this is just a wrapper around the current BeanFactory.
ubic.gemma.core.util.AbstractSpringAwareCLI.getPersisterHelper()
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getFactorValuesUsed()	This was renamed for clarity.
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getDownregulatedCount()	use DiffExResultSetSummaryValueObject.getNumberOfDownregulatedProbes() instead.
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getResultSetId()	use #getId() instead
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getUpregulatedCount()	use DiffExResultSetSummaryValueObject.getNumberOfUpregulatedProbes() instead.
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isEditable()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isOwnedByCurrentUser()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isPublic()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isShared()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setEditable(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setOwnedByCurrentUser(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setPublic(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setShared(boolean)
ubic.gemma.model.common.search.SearchSettings.getTermUri()	use SearchSettings.getQuery() and SearchSettings.isTermQuery() instead.
ubic.gemma.model.common.search.SearchSettings.setTermUri(String)	URI can be set with #setQuery(String) instead.
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getExpressionExperimentCount()	use ArrayDesignValueObject.getNumberOfExpressionExperiments() instead.
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getTaxonID()	use #getTaxonObject() instead
ubic.gemma.model.expression.biomaterial.BioMaterialValueObject.getFactorValueObjects()	use BioMaterialValueObject.getFactorValues()
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getBioAssayCount()	use #getNumberOfBioAssays() instead.
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getTaxonId()	use #getTaxonObject() instead
ubic.gemma.model.expression.experiment.FactorValue.getValue()	use FactorValue.getCharacteristics() instead.
ubic.gemma.model.expression.experiment.FactorValue.setValue(String)	use FactorValue.setCharacteristics(Set) ()} instead.
ubic.gemma.model.genome.gene.GeneProductValueObject.getNucleotideEnd()
ubic.gemma.model.genome.gene.GeneProductValueObject.setNucleotideEnd(Long)
ubic.gemma.persistence.service.AbstractDao.reattach(T)
ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl.loadValueObjects(Collection<ExpressionExperimentSet>)	extremely inefficient for EESets, use ExpressionExperimentSetDaoImpl.loadValueObjects(Collection, boolean) if possible.
ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService.remove(Collection<ProcessedExpressionDataVector>)	never use this method, you can use ProcessedExpressionDataVectorService.removeProcessedDataVectors(ExpressionExperiment) instead, or clear ExpressionExperiment.getProcessedExpressionDataVectors() directly. The relationship is actually managed by Hibernate.
ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService.remove(Collection<RawExpressionDataVector>)	never use this method, instead clear ExpressionExperiment.getProcessedExpressionDataVectors() directly. The relationship is actually managed by Hibernate.
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueService.findByValue(String)
ubic.gemma.persistence.service.genome.GeneDao.findByPhysicalLocation(PhysicalLocation)
ubic.gemma.persistence.util.Slice.add(O)
ubic.gemma.persistence.util.Slice.remove(Object)
ubic.gemma.persistence.util.SpringContextUtil.getApplicationContext(boolean, boolean, String[])	this method does not support producing Gemma Web contexts, please migrate existing code to use SpringContextUtil.getApplicationContext(boolean, String...) instead.
ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController.addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>, Boolean)
ubic.gemma.web.controller.GeneralSearchControllerImpl.showForm(HttpServletRequest, HttpServletResponse, BindException)
ubic.gemma.web.controller.genome.gene.GeneSetController.addSessionGroups(Collection<SessionBoundGeneSetValueObject>, Boolean)
ubic.gemma.web.controller.genome.gene.GeneSetController.removeSessionGroups(Collection<SessionBoundGeneSetValueObject>)
ubic.gemma.web.controller.genome.gene.GeneSetController.updateSessionGroups(Collection<SessionBoundGeneSetValueObject>)

Constructors

Constructor	Description
ubic.gemma.model.expression.experiment.FactorValueValueObject(FactorValue, Characteristic)	see class deprecated note